Frequently asked questions about our microarray services

Microarray Service FAQs

Advances in microarray technologies have enabled efficient characterization of the genetic variation, empowering researchers to better understand the underlying mechanisms of genetic disease and phenotypic characterization.

Our services deliver a comprehensive analysis solution across multiple species and genetic variation.

Illumina FastTrack Services combines high performance Illumina platforms with expert Illumina scientists; we deliver high-quality genotyping and sequencing data to support your research projects. You’ll reap the benefits of our Illumina technology, with a personalized service that delivers your data quickly and at a reasonable cost. FastTrack Services offer a range of products from whole genome Genotyping to custom content genotyping, whole Genome Sequencing, phasing and long-read sequencing.

For genotyping, we require at least 1.75 μg of pure and intact DNA per sample in 35ul (minimum concentration of 50ng/ul as measured by picogreen). For methylation, we require at least 2.10 ug of pure and intact DNA per sample in 40ul (minimum concentration of 70ng/ul as measured by picogreen). Sample submission guides: Genotyping Guide | Methylation Guide

Once the Illumina FastTrack Services Team receives your signed contract, you will be contacted by aproject manager. This person is assigned to your project and will guide you throughout the process to adequately prepare and submit your samples to our lab, and design your SNP panel for customproducts. The project manager is responsible for tracking your samples though the lab and will be available throughout your project to answer any questions you might have about processes, samples or deliverables.

The project manager will assist you in the design of your SNP panel. This process is a collaborative work where the project manager uses Illumina design software to assess feasibility of SNP lists that you will provide in the form of rsIDs or Sequence submissions for novel SNPs or non-human panels. For each submission, you will be provided with a feasibility assessment as well as tag marker selection for haplotype blocks and genes annotations. Once you have selected your final SNP list, the project manager takes the responsibility to order the beadpool for you.

Samples are quantified upon arrival in our lab using Picogreen quantification. They proceed through our genotyping or methylation workflow which is fully automated and integrated with Illumina LIMS to ensure positive sample tracking. Upon completion of every project, a project manager assesses the quality of every sample and marker performance to identify those that do not perform well. For genotyping projects, genotype calls are optimized through cluster editing and reports are created to be sent as part of the project deliverables.

Your Project Scientist will work with you to submit some representative test samples. These samples will be quantitated at Illumina using PicoGreen to confirm sample concentration. Samples will be genotyped on an Illumina array to determine genotyping quality. This data set is not for distribution; rather, it is used exclusively for sample quality determination. Upon successful quality determination, the Illumina Project Scientist will work with you to submit the Production samples.

The Illumina microarray services lab will repeat all samples that have adequate concentrations but low genotyping quality. This ensures that each sample is given at least two genotyping attempts to optimize data quality. There is no charge for second attempts, but you will be charged for all samples attempted.

As part of the deliverable, each customer is provided a seat license for Illumina’s GenomeStudio software. All samples and markers are provided in a GenomeStudio project workspace. The Project Scientist zeros poorly performing samples and markers; however, these remain available, enabling customers to make their own determination. Provided genotyping data files indicate the bi-allelic genotyping call with each genotype on a separate row. The exported data files are customizable such that the Project Scientist will ask customers for their preference before delivery. Optional data fields include intensity values, allelic strand formats etc. Intensity files, locus and DNA summary files showing project statistics are also delivered. All data is delivered via a secure FTP site. Ongoing support from the project scientist will be provided should any questions remain about the data.

Throughout our process your samples go through multiple quality control steps and quality results are compared to internal controls for accuracy verification. We list below some of the parameters we look at:

  • For DNA samples, we graph the call rates and the GenCall score. Outlying samples typically have poor quality.
  • For Human samples on Standard arrays, the Call rate cut-off for sample quality is above 99%. Quality cut-offs can vary by sample species, product used etc.
  • In some cases, samples have apparently poor quality for genetic reasons. Your project manager will work with you to understand the study and downstream ramifications.
  • For marker quality, the project manager will look at several metrics to investigate clustering quality. Some of those metrics include call rate, reproducibility, cluster separation, Hardy-Weinberg when applicable, intensity levels, etc. The goal is to identify poorly performing samples as well as markers that have not clustered well and should either be ‘zeroed’ or edited.

If you are interested in a project with Illumina Fast Track Services, please contact your sales representative or get a quote. One of Illumina’s Sales Representatives will discuss your genotyping project and will help you select the product that best fit your needs and will provide you a quote. A Project Manager will contact you to discuss your project and shipping details once the quote has been processed.

Prices vary depending on the selected product and the requested number of samples. Please contact your sales representative or get a quote and a sales representative will contact you.

Turnaround time is dependent on the selected product and the requested number of samples. Additionally, it is dependent on selection of Loci as applicable and receipt of samples. Please reference our estimated turnaround time as shown on Microarray Service Process page. Please contact your sales representative or submit your question through our website.

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